Nora

It was consistent, and then the two changes happened in the wrong order. That is the whole story in a sentence.

It was consistent, and then two things happened in the wrong order.

The spelling was largely reasonable when it was set down. In Middle English, the letters mostly corresponded to sounds. The silent k in knight was pronounced. The gh was a real consonant, a sound at the back of the throat, still present in some dialects and in related languages.

Then the pronunciation changed enormously and the spelling did not follow.

The biggest single cause is a large shift in the long vowels over roughly the fifteenth to seventeenth centuries. The vowels moved systematically, the sound written as an i became the diphthong we now say in time, and so on. Every long vowel ended up representing a different sound from the one it originally denoted, which is why the vowel letters in English match no other European language.

At the same time various consonants stopped being pronounced, the k in knight, the gh in night, the l in walk.

So the spelling is not arbitrary at all. It is a reasonably accurate record of how the language sounded several hundred years ago. You are reading a snapshot of a pronunciation nobody uses any more, and the through-though-tough family is the clearest fossil of it.